Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

Cell type Class
Breast
Cell type
CAL-120
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
breast cancer cells
treatment
Infigratinib_2d
cell line
CAL-120
chip antibody
BRG1
chip antibody manufacturer
abcam
chip antibody catalog number
Ab110641

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were then lysed with 1% SDS lysis buffer (1% SDS, 10mM EDTA (pH=8), 50mM Tris-HCl (pH=8)) containing protease and deacetylase inhibitors, and sonicated for 5 min with settings of PIP 140, DF 5%, cpb 200 on a Covaris E220 (Covaris Inc., Woburn, MA) to obtain 200-600bp chromatin fragments. libraries were constructed from 2 ng of DNA, using the ThruPLEX DNA-seq kit (#R400427, Rubicon Genomics), according to the manufacturer's protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers' protocols; ChIP-seq libraries were uniquely indexed in equimolar ratios, and sequenced to a target depth of 40M reads on an Illumina NextSeq500 run, with single-end 75bp reads.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
9809747
Reads aligned (%)
66.5
Duplicates removed (%)
13.5
Number of peaks
135 (qval < 1E-05)

hg19

Number of total reads
9809747
Reads aligned (%)
66.0
Duplicates removed (%)
15.0
Number of peaks
156 (qval < 1E-05)

Base call quality data from DBCLS SRA